Archiving of vectors

ABSTRACT

The invention relates to a solid medium or matrix for storage of nucleic acid molecules (e.g. RNA and/or DNA), particularly vectors and especially plasmids, comprising a solid matrix preferably having a compound or composition which protects against degradation of nucleic acids incorporated into or absorbed on the matrix. The invention also relates to methods for storage or isolation/purification of nucleic acids using this solid medium, and in situ use of the stored or isolated/purified nucleic acids.

CROSS REFERENCE TO RELATED APPLICATIONS

The present application is a continuing divisional application of U.S.patent application Ser. No. 09/354,664, filed Jul. 16, 1999, now U.S.Pat. No. 6,750,059, issued Jun. 15, 2004, which claims the benefit ofthe filing dates of U.S. Application Nos. 60/093,073, filed Jul. 16,1998, and 60/100,737, filed Sep. 17, 1998, the disclosures of which areincorporated by reference herein in their entireties.

BACKGROUND AND SUMMARY OF THE INVENTION

The present invention relates to a solid medium or support for use inthe storage (preferably the long term storage) of nucleic acids (e.g.DNA and RNA, ribosomal RNA and messenger RNA), particularly one or morevectors and especially one or more plasmids, and to methods whichcomprise the use of this solid medium or support. In particular, theinvention relates to a method for storage and transport of such nucleicacids or vectors on the solid medium, as well as to methods whichinvolve either recovery or purification of the nucleic acids or vectorsfrom the solid medium, or the use or manipulation of the nucleic acidsor vectors obtained from or contained by or on the solid medium. Suchuse or manipulation includes, for example, digestion (e.g. with one ormore nucleases, exonucleases or endonucleases such as restrictionenzymes), synthesis (e.g. with one or more polymerases and/or reversetranscriptases), amplification (e.g. by polymerase chain reaction withone or more polymerases), sequencing (e.g. with one or morepolymerases), or transformation or transfection into one or more hostcells using, for example, chemically competent or electrocompetent cellsor using known transfection reagents and techniques. The preferredmedium or support is a matrix which protects against degradation ofnucleic acid incorporated onto the matrix. Such a matrix may comprise anabsorbent cellulose-based matrix or paper, or a micromesh of syntheticplastic material such as those described in U.S. Pat. No. 5,496,562,which is incorporated by reference herein. Preferably, the matrixcomprises a composition comprising a weak base, a chelating agent, ananionic surfactant or anionic detergent, and optionally uric acid or aurate salt, wherein said composition is absorbed on or incorporated intosaid matrix. FTA® paper brand cellulose based solid matrix, andderivatives, variants and modifications thereof are included among suchsupports.

Another aspect of the invention relates to such a solid medium orsupport for use in the sampling, purifying and/or analyzing of one ormore non-chromosomal DNA (e.g. mitochondria, chloroplast, F′) and tomethods which comprise the use of this solid medium or support for suchpurposes.

For many projects, generation of numerous DNA samples from biologicalspecimens is routine. Handling and archiving a large collection canbecome a logistical problem for the laboratory. One solution, used inforensic labs, is the blood-storage medium cellulose based solid matrixpaper card, such as an FTA® Card. A cellulose based solid matrix papercard stores genomic DNA in the form of dried spots of human whole blood,the cells of which were lysed on the paper. Stored at room temperature,genomic DNA on a cellulose based solid matrix paper is reported to bestable, e.g., for at least 7.5 years using an FTA® Card brand cellulosebased solid matrix (Burgoyne, et al., Conventional DNA Collection andProcessing: Disposable Toothbrushes and FTA® Paper as a Non-threatingBuccal-Cell Collection Kit Compatible with Automatable DNA Processing,8^(th) International Symposium on Human Identification, Sep. 17-20,1997). Before analysis of the captured DNA, a few simple washing stepsremove the stabilizing chemicals and cellular inhibitors of enzymaticreactions. Since the DNA remains with the paper, the manipulations topurify the DNA are simplified and amenable to automation. DNA samples oncellulose-based solid matrix cards offer a very compact archival systemcompared to glass vials or plastic tubes located in precious freezerspace.

Bacterial DNAs spotted on cellulose based solid matrix cards may be anefficient system for storage and retrieval as well. Recently, Rogers andBurgoyne characterized by PCR-ribotyping culture samples of severalbacterial strains of Staphylococcus and E. coli stored on FTA® Cardsbrand cellulose based solid matrix (Rogers, et al., (1997) Anal.Biochem. 247:223). Further, purified plasmid DNA was efficientlyrecovered after spotting on treated paper, however, encasement of thepaper in polystyrene was used for storage (Burgoyne, U.S. Pat. No.5,496,562, which is incorporated by reference herein).

According to the present invention, any nucleic acids (e.g. RNA and DNAand particularly RNA and DNA vectors) may be archived and laterrecovered and/or manipulated by a simple and efficient method in whichthe host carrying the one or more nucleic acids or vectors are contactedwith a solid medium (preferably FTA® paper brand cellulose based solidmatrix or derivatives, variants or modifications thereof), without theneed to encase the support or use protective coatings (such aspolystyrene) to store the nucleic acids or vectors. Thus, the inventionavoids the need to use organic solvents or harsh chemicals to removesuch protective coatings before use, manipulation, purification orisolation of the nucleic acid molecules or vectors can take place. Inanother aspect, purified nucleic acid molecules or vectors may be used,although in a preferred aspect, crude preparations (unpurified vectorpreparations) containing the one or more nucleic acid molecules orvectors may be contacted with the solid medium or support. Thus, theinvention provides methods to isolate and/or purify nucleic acidmolecules or vectors from any sample containing one or more vectors suchas host cells, viruses, viral plaques, and/or crude preparations frombiological materials (such as host cell or virus extracts, lysates,debri, hydrolysates, and the like). Such isolated and/or purifiednucleic acid molecules or vectors obtained from or contained by thesolid support or matrix may be used or manipulated in one or morestandard molecular biology techniques, such as digestion, sequencing,amplification, synthesis and transformation/transfection reactions. In aparticularly preferred aspect, one or more host cells containing thenucleic acid molecules or vectors to be isolated, stored and/ormanipulated can be contacted directly with the medium or support.According to the present invention, host cell cultures or colonies fromplates may be used. Preferred host cells for use in the inventioninclude prokaryotic or eukaryotic host cells, particularly gram positiveand gram negative bacteria such as Escherichia, Streptomyces,Pseudomonas, and the like.

Other preferred embodiments of the present invention will be apparent toone of ordinary skill in light of what is known in the art, in light ofthe following drawings and description of the invention, and in light ofthe claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a PCR analysis of bacterial genomic DNA on an FTA® Card. Theagarose gel analysis of the amplification products pictured are shown asfollows: lanes 1-3: Agrobacter tumefaciens strain LBA4404; lanes 4-6:Agrobacter tumefaciens strain EHA101; lanes 7-9: E. coli DH10B strain;lanes 10-12: Streptomyces coelicolor; lanes 13-15: S. lividans; andlanes 16-18: S. paralus. Molecular size standards are a Low DNA Mass™Ladder (M1) and a 1 Kb DNA Ladder (M2).

FIG. 2 is a PCR analysis of plasmid DNA from E. coli (DH10B) on an FTA®Card.

FIG. 3 is a PCR analysis of plasmid and genomic DNA from Saccharomycescerevisiae on an FTA® Card.

DETAILED DESCRIPTION OF THE INVENTION

In the description that follows, a number of terms used in the fields ofmolecular biology and recombinant DNA technology are utilizedextensively. In order to provide a clearer and consistent understandingof the specification and claims, including the scope to be given suchterms, the following definitions are provided.

Amplification. As used herein, “amplification” refers to any in vitromethod for increasing the number of copies of a nucleotide sequence withthe use of a polymerase. Nucleic acid amplification results in theincorporation of nucleotides into a nucleic acid (e.g., DNA) molecule orprimer thereby forming a new nucleic acid molecule complementary to thenucleic acid template. The formed nucleic acid molecule and its templatecan be used as templates to synthesize additional nucleic acidmolecules. As used herein, one amplification reaction may consist ofmany rounds of nucleic acid synthesis. Amplification reactions include,for example, polymerase chain reactions (PCR). One PCR reaction mayconsist of 5 to 100 “cycles” of denaturation and synthesis of a nucleicacid molecule.

Polymerases (including DNA polymerases and RNA polymerases) useful inaccordance with the present invention include, but are not limited to,Thermus thermophilus (Tth) DNA polymerase, Thermus aquaticus (Taq) DNApolymerase, Thermotoga neopolitana (Tne) DNA polymerase, Thermotogamaritima (Tma) DNA polymerase, Thermococcus litoralis (Tli or VENT™) DNApolymerase, Pyrococcus furiosus (Pfu) DNA polymerase, DEEPVENT™ DNApolymerase, Pyrococcus woosii (Pwo) DNA polymerase, Bacillussterothermophilus (Bst) DNA polymerase, Bacillus caldophilus (Bca) DNApolymerase, Sulfolobus acidocaldarius (Sac) DNA polymerase, Thermoplasmaacidophilum (Tac) DNA polymerase, Thermus favus (Tfl/Tub) DNApolymerase, Thermus ruber (Tru) DNA polymerase, Thermus brockiahus(DYNAZYME™) DNA polymerase, Methanobacterium thermoautotrophicum (Mth)DNA polymerase, mycobacterium DNA polymerase (Mtb, Mlep), and mutants,and variants and derivatives thereof. RNA polymerases such as T3, T5 andSP6 and mutants, variants and derivatives thereof may also be used inaccordance with the invention.

Polymerases used in accordance with the invention may be any enzyme thatcan synthesize a nucleic acid molecule from a nucleic acid template,typically in the 5′ to 3′ direction. The nucleic acid polymerases usedin the present invention may be mesophilic or thermophilic, and arepreferably thermophilic. Preferred mesophilic DNA polymerases include T7DNA polymerase, T5 DNA polymerase, Klenow fragment DNA polymerase, DNApolymerase III and the like. Preferred thermostable DNA polymerases thatmay be used in the methods of the invention include Taq, Tne, Tma, Pfu,Tfl, Tth, Stoffel fragment, VENT™″ and DEEPVENT™ DNA polymerases, andmutants, variants and derivatives thereof (U.S. Pat. No. 5,436,149; U.S.Pat. No. 4,889,818; U.S. Pat. No. 4,965,188; U.S. Pat. No. 5,079,352;U.S. Pat. No. 5,614,365; U.S. Pat. No. 5,374,553; U.S. Pat. No.5,270,179; U.S. Pat. No. 5,047,342; U.S. Pat. No. 5,512,462; WO92/06188; WO 92/06200; WO 96/10640; Barnes, W. M., Gene 112:29-35(1992); Lawyer, F. C., et al., PCR Meth. Appl. 2:275-287 (1993); Flaman,J.-M, et al., Nucl. Acids Res. 22(15):3259-3260 (1994)). Foramplification of long nucleic acid molecules (e.g., nucleic acidmolecules longer than about 3-5 Kb in length), at least two DNApolymerases (one substantially lacking 3′ exonuclease activity and theother having 3′ exonuclease activity) are typically used. See U.S. Pat.No. 5,436,149; and U.S. Pat. No. 5,512,462; Barnes, W. M., Gene112:29-35 (1992), the disclosures of which are incorporated herein intheir entireties. Examples of DNA polymerases substantially lacking in3′ exonuclease activity include, but are not limited to, Taq, Tne(exo⁻),Tma(exo⁻), Pfu(exo⁻), Pwo(exo⁻) and Tth DNA polymerases, and mutants,variants and derivatives thereof.

Host. Any prokaryotic or eukaryotic cell that is the recipient of areplicable expression vector or cloning vector. The terms “host” or“host cell” may be used interchangeably herein. For examples of suchhosts, see Maniatis et al., Molecular Cloning: A Laboratory Manual, ColdSpring Harbor Laboratory, Cold Spring Harbor, N.Y. (1982). Preferredprokaryotic hosts include, but are not limited to, bacteria of the genusEscherichia (e.g. E. coli), Bacillus, Staphylococcus, Agrobacter (e.g.A. tumefaciens), Streptomyces, Pseudomonas, Salmonella, Serratia,Caryophanon, etc. The most preferred prokaryotic host is E. coli.Bacterial hosts of particular interest in the present invention includeE. coli K12, DHIOB, DH5α, and HB 101. Preferred eukaryotic hostsinclude, but are not limited to, fungi, fish cells, yeast cells, plantcells and animal cells. Particularly preferred animal cells are insectcells such as Drosophila cells, Spodoptera Sf9 and Sf21 cells andTrichoplusa High-Five cells; nematode cells such as C. elegans cells;and mammalian cells such as COS cells, CHO cells, VERO cells, 293 cells,PERC6 cells, BHK cells and human cells.

Vector. A vector is a nucleic acid molecule (preferably DNA) capable ofreplicating autonomously in a host cell. Such vectors may also becharacterized by having a small number of endonuclease restriction sitesat which such sequences may be cut without loss of an essentialbiological function and into which nucleic acid molecules may be splicedto bring about its replication and cloning. Examples include plasmids,autonomously replicating sequences (ARS), centromeres, cosmids andphagemids. Vectors can further provide primer sites, e.g., for PCR,transcriptional and/or translational initiation and/or regulation sites,recombinational signals, replicons, etc. The vector can further containone or more selectable markers suitable for use in the identification ofcells transformed or transfected with the vector, such as kanamycin,tetracycline, amplicillin, etc.

In accordance with the invention, any vector may be used. In particular,vectors known in the art and those commercially available (and variantsor derivatives thereof) may be used in accordance with the invention.Such vectors may be obtained from, for example, Vector LaboratoriesInc., InVitrogen, Promega, Novagen, NEB, Clontech, Boehringer Mannheim,Pharmacia, EpiCenter, OriGenes Technologies Inc., Stratagene, PerkinElmer, Pharmingen, Life Technologies, Inc., and Research Genetics. Suchvectors may then for example be used for cloning or subcloning nucleicacid molecules of interest. General classes of vectors of particularinterest include prokaryotic and/or eukaryotic cloning vectors,expression vectors, fusion vectors, two-hybrid or reverse two-hybridvectors, shuttle vectors for use in different hosts, mutagenesisvectors, transcription vectors, vectors for receiving large inserts andthe like.

Other vectors of interest include viral origin vectors (M13 vectors,bacterial phage λ vectors, baculovirus vectors, adenovirus vectors, andretrovirus vectors), high, low and adjustable copy number vectors,vectors which have compatible replicons for use in combination in asingle host (pACYC184 and pBR322) and eukaryotic episomal replicationvectors (pCDM8).

Particūlar vectors of interest include prokaryotic expression vectorssuch as pcDNA II, pSL301, pSE280, pSE380, pSE420, pTrcHisA, B, and C,pRSET A, B, and C (Invitrogen, Inc.), pGEMEX-1, and pGEMEX-2 (Promega,Inc.), the pET vectors (Novagen, Inc.), pTrc99A, pKK223-3, the pGEXvectors, pEZZ18, pRIT2T, and pMC1871 (Pharmacia, Inc.), pKK233-2 andpKK388-1 (Clontech, Inc.), and pProEx-HT (Life Technologies, Inc.) andvariants and derivatives thereof. Vectors can also be eukaryoticexpression vectors such as pFastBac, pFastBac HT, pFastBac DUAL, pSFV,and pTet-Splice (Life Technologies, Inc.), pEUK-Cl, pPUR, pMAM, pMAMneo,pBI101, pBI121, pDR2, pCMVEBNA, and pYACneo (Clontech), pSVK3, pSVL,pMSG, pCH110, and pKK232-8 (Pharmacia, Inc.), p3′SS, pXTI, pSG5, pPbac,pMbac, pMC1neo, and pOG44 (Stratagene, Inc.), and pYES2, pAC360,pBlueBacHis A, B, and C, pVL1392, pBsueBacIII, pCDM8, pcDNAI, pZeoSV,pcDNA3 pREP4, pCEP4, and pEBVHis (Invitrogen, Inc.) and variants orderivatives thereof.

Other vectors of particular interest include pUC 18, pUC 19,pBlueScript, pSPORT, cosmids, phagemids, fosmids (pFOSI), YAC's (yeastartificial chromosomes), BAC's (bacterial artificial chromosomes), pBAC108L, pBACe3.6, pBeloBACl1 (Research Genetics), PACs, P1 (E. coliphage), pQE70, pQE60, pQE9 (Qiagen), pBS vectors, PhageScript vectors,BlueScript vectors, pNH8A, pNH16A, pNH18A, pNH46A (Stratagene), pcDNA3(InVitrogen), pGEX, pTrsfus, pTrc99A, pET-5, pET-9, pKK223-3, pKK233-3,pDR540, pRIT5 (Pharmacia), pSPORT1, pSPORT2, pCMVSPORT2.0, pSV-SPORT1(Life Technologies, Inc.), and the vectors described in ProvisionalPatent Application No. 60/065,930, filed Oct. 24, 1997, the entirecontents of which is herein incorporated by reference, and variants orderivatives thereof.

Additional vectors of interest include pTrxFus, pThioHis, pLEX, pTrcHis,pTrcHis2, pRSET, pBlueBacHis2, pcDNA3.1/His, pcDNA3.1(−)/Myc-His,pSecTag, pEBVHis, pPIC9K, pPIC3.5K, pAO815, pPICZ, pPICZα, pGAPZ,pGAPZα, pBlueBac4.5, pBlueBacHis2, pMelBac, pSinRep5, pSinHis, pIND,pIND(SP1), pVgRXR, pcDNA2.1. pYES2, pZErO1.1, pZErO-2.1, pCR-Blunt,pSE280, pSE380, pSE420, pVL1392, pVL1393, pCDM8, pcDNA1.1, pcDNA1.1/Amp,pcDNA3.1, pcDNA3.1/Zeo, pSe, SV2, pRc/CMV2, pRc/RSV, pREP4, pREP7,pREP8, pREP9, pREP10, pCEP4, pEBVHis, pCR3.1, pCR2.1, pCR3.1-Uni, andpCRBac from Invitrogen; λExCell, λ gt11, pTrc99A, pKK223-3, pGEX-1λT,pGEX-2T, pGEX-2TK, pGEX-4T-1, pGEX-4T-2, pGEX-4T-3, pGEX-3X, pGEX-5X-1,pGEX-5X-2, pGEX-5X-3, pEZZ18, pRIT2T, pMC1871, pSVK3, pSVL, pMSG,pCH110, pKK232-8, pSL1180, pNEO, and pUC4K from Pharmacia;pSCREEN-lb(+), pT7Blue(R), pT7Blue-2, pCITE-4-abc(+), pOCUS-2, pTAg,pET-32 LIC, pET-30 LIC, pBAC-2cp LIC, pBACgus-2 cp LIC, pT7Blue-2 LIC,pT7Blue-2, λSCREEN-1, λBlueSTAR, pET-3abcd, pET-7abc, pET9abcd,pET11abcd, pET12abc, pET-14b, pET-15b, pET-16b, pET-17b-pET-17xb,pET-19b, pET-20b(+), pET-21abcd(+), pET-22b(+), pET-23abcd(+),pET-24abcd(+), pET-25b(+), pET-26b(+), pET-27b(+), pET-28abc(+),pET-29abc(+), pET-30abc(+), pET-31b(+), pET-32abc(+), pET33b(+), pBAC-1,pBACgus-1, pBAC4x-1, pBACgus4x-1, pBAC-3 cp, pBACgus-2 cp, pBACsurf-1,plg, Signal plg, pYX, Selecta Vecta-Neo, Selecta Vecta-Hyg, and SelectaVecta-Gpt from Novagen; pLexA, pB42AD, pGBT9, pAS2-1, pGAD424, pACT2,pGAD GL, pGAD GH, pGAD10, pGilda, pEZM3, pEGFP, pEGFP-1, pEGFP—N,pEGFP-C, pEBFP, pGFPuv, pGFP, p6xHis-GFP, pSEAP2-Basic, pSEAP2-Contral,pSEAP2-Promoter, pSEAP2-Enhancer, pβgal-Basic, pβgal-Control,pβgal-Promoter, pβ-Enhancer, pCMVβ, pTet-Off, pTet-On, pTK-Hyg,pRetro-Off, pRetro-On, pIRES1neo, pIRES1hyg, pLXSN, pLNCX, pLAPSN,pMAMneo, pMAMneo-CAT, pMAMneo-LUC, pPUR, pSV2neo, pYEX 4T-1/2/3,pYEX-S1, pBacPAK-His, pBacPAK8/9, pAcUW31, BacPAK6, pTriplEx, λgt10,λgtl1, pWE15, and λTriplEx from Clontech; Lambda ZAP II, pBK-CMV,pBK-RSV, pBluescript II KS +/−, pBluescript II SK +/−, pAD-GAL4,pBD-GAL4 Cam, pSurfscript, Lambda FIX II, Lambda DASH, Lambda EMBL3,Lambda EMBL4, SuperCos, pWE15, pCR-Scrigt Amp, pCR-Script Cam,pCR-Script Direct, pBS +/−, pBC KS +/−, pBC SK +/−, Phagescript,pCAL-n-EK, pCAL-n, pCAL-c, pCAL-kc, pET-3abcd, pET-11abcd, pSPUTK,pESP-1, pCMVLacl, pOPRSVI/MCS, pOPI3 CAT, pXT1, pSG5, pPbac, pMbac,pMClneo, pMClneo Poly A, pOG44, pOG45, pFRTβGAL, pNEOβGAL, pRS403,pRS404, pRS405, pRS406, pRS413, pRS414, pRS415, and pRS416 fromStratagene, and derivatives or variants thereof.

Two-hybrid and reverse two-hybrid vectors of particular interest includepPC86, pDBLeu, pDBTrp, pPC97, p2.5, pGAD1-3, pGAD10, pACt, pACT2,pGADGL, pGADGH, pAS2-1, pGAD424, pGBT8, pGBT9, pGAD-GAL4, pLexA,pBD-GAL4, pHISi, pHISi-1, placZi, pB42AD, pDG202, pJK202, pJG4-5,pNLexA, pYESTrp and variants or derivatives thereof.

Storage. As used herein, “storage” refers to maintaining thesupport/vectors for a period of time at a temperature or temperatures ofinterest. Preferably, storage is accomplished at about 20 to 30° C.(preferably room temperature, e.g. 25° C.), but may be at higher orlower temperatures depending on the need. Lower storage temperatures mayrange from about 0 to 20° C., −20 to 0° C., and −80 to −20° C. Long termstorage in accordance with the invention is greater than one year,preferably greater than 2 years, still more preferably greater than 3years, still more preferably greater than 5 years, still more preferablygreater than 10 years, and most preferably greater than 15 years.

Other terms used in the fields of recombinant DNA technology andmolecular and cell biology as used herein will be generally understoodby one of ordinary sill in the applicable arts.

It will be understood by one of ordinary skill in the relevant arts thatother suitable modifications and adaptations to the methods andapplications described herein are readily apparent from the descriptionof the invention contained herein in view of information known to theordinarily skilled artisan, and may be made without departing from thescope of the invention or any embodiment thereof. Having now describedthe present invention in detail, the same will be more clearlyunderstood by reference to the following examples, which are includedherewith for purposes of illustration only and are not intended to belimiting of the invention.

EXAMPLES

All reagents were from Life Technologies, Inc., Rockville, Md., unlessotherwise noted. The cellulose based solid matrix used was an FTA® paperor FTA® Card brand cellulose based solid matrix unless otherwise noted.

Example 1

Preparation of Samples on an FTA® Card. From bacterial cultures grownovernight, 5 ul were spotted in separate locations on an FTA® Card brandcellulose based solid matrix (Cat. No. 10786) and allowed to dryovernight at room temperature. Bacterial colonies from petri dishes werespotted onto an FTA® Card brand cellulose based solid matrix bysuspending a colony in 5 μl of PBS, applying the entire volume as asingle spot, then allowing the paper to dry overnight at roomtemperature.

For yeast genomic DNA and yeast plasmid (two-hybrid) DNAs, plates wereobtained which had several colonies of each 2 two-hybrid (ProQuest, Cat.No. 10835-023) control strain. From each plate, several individualcolonies were taken. Each individual colony was suspended in 5 μl PBSand each 5 μl aliquot was spotted in individual spots onto an FTA® Cardbrand cellulose based solid matrix.

Using a HARRIS MICRO PUNCH™ Apparatus with mat, a 2-mm punch was takenfrom a dried bacterial or yeast spot (˜6 mm diameter), then washed withFTA® Purification Reagent (Cat. No. 10876) and TE buffer according tomanufacturer's recommendations. The washed punch was air dried for 1hour at room temperature or 30 min at 60° C. Processed cellulose basedsolid matrix card punches were either assayed immediately or stored at4° C.

Amplification. DNA was amplified directly from a washed FTA® Card brandcellulose based solid matrix punch placed in 50 μl of 1×PCR buffer, 1.5mM Mg⁺⁺, 0.2 μM dNTPs, 1.25 units Platinum™ Taq DNA Polymerase, and 0.2μM primers (Table 1). For Agrobacter tumefaciens genomic sequence,amplification was: one cycle of 94° C. for 1 min, 30 cycles of 94° C.for 1 min., 55° C. for 30 s, 72° C. for 3 min and one cycle of 72° C.for 10 min. For E. coli DH10B™ genomic DNA and Streptomyces samples,amplification was: one cycle of 94° C. for 1 min, 36 cycles of 94° C.for 30 s, 55° C. for 1 min, 72° C. for 1 min, and one cycle of 72° C.for 10 min.

TABLE 1 Primer sequences Amplicon Target Size (bp) Primer SequenceAgrobacter 16S rRNA 284 GGGAA AGATT TATCG GGGAT G tumefaciens GGCTGCTGGC ACGAA GTTA (SEQ ID NO: 1) E. coli DH10B cells rrsE 372 CTGAG ACACGGTCCA GACTC CTACG TCACC GCTAC ACCTG GGATT CTACC (SEQ ID NO: 2)Streptomyces 165 rRNA 1500 AGAGT TTGAT GATCC TGGCT CAG AAGGA GGTGA TCCAGCCGCA (SEQ ID NO: 3) Plasmid pSUsrmB2 1503 CCCAG TCACG ACGTT GTAAA ACGAGCGG ATAAC AATTT CACAC AGG (SEQ ID NO: 4) Plasmid pMAB32 1800 GAATAAGTGC GACAT CATCA TC GTAAA TTTCT GGCAA GGTAG AC (SEQ ID NO: 5) PlasmidpJH11104 1200 ACTTC TTCGC CCCCG TTTTC GCTGA CTTGA CGGGA CGGCG (SEQ IDNO: 6)

Plasmids pSUsrmB2 and pJH11104 were amplified in the same reactionmixture described above. Amplification of pMAB32 was in a reactionmixture using eLONGase™ Amplification System at 1.5 mm Mg⁺⁺. For allthree plasmids, the incubation profile was one cycle of 94° C. for 1min, one cycle of 94° C. for 15 s, and 30 cycles of 94° C. for 15 s, 55°C. for 30 s, 72° C. for 3 min.

For yeast (Saccharomyces cerevisiae) plasmid and genomic amplifications,reaction conditions using eLONGase™ Amplification System were: one cycleof 94° C. for 2 min, 40 cycles of 94° C. for 15 s, 55° C. for 20 s, 72°C. for 5 min. Primer sequences used for yeast amplification are shown inTable 2.

TABLE 2 Primer sequences Amplicon Target Size (bp) Primer SequencePlasmid pPC97 255 GAATA AGTGC GACAT CATCA TC Plasmid pPC97-RB 2088 GTAAATTTCT GGCAA GGTAG AC Plasmid pPC97-dE2F 834 (SEQ ID NO: 5) PlasmidpPC97-Fos 447 Plasmid pCL1 2853 Saccharomyces SPAL promoter 350 GCGAGGCATA TTTAT GGTGA AGG cerevisiae CATTT CCGTG CAAAG GTACT AACMaV203(MATa) (SEQ ID NO: 7)

Aliquots of each reaction product were analyzed by electrophoresis in a1.5% (w/v) agarose/TAE gel.

Transformation. Cells were transformed with plasmid DNA from washed FTA®Card brand cellulose based solid matrix punches, either by adding apunch directly to the reaction or by adding 5 μl of a TE buffer extract,which had soaked the punch for 20 min. at room temperature. Both MAXEfficiency DH5α™ and MAX Efficiency DH10B cells were transformedaccording to manufacturer's recommendations. Various dilutions of thefinal 1-ml transformation reaction volume (100 μl of a 1/100 dilution,100 μl of a 1/10 dilution, 100 μl of undiluted cells, and 10 μl ofundiluted cells) were plated on the appropriate media and incubatedovernight at 37° C.

Using samples from overnight liquid cultures spotted on FTA® Cards brandcellulose based solid matrix, Rogers and Burgoyne generated the expecteddiagnostic PCR patterns for each of six bacterial strains tested(Rogers, et al., (1997) Anal. Biochem. 247:223). However, according tothe present invention, bacterial colonies placed on an FTA® Card brandcellulose based solid matrix were tested. Unlike Rogers and Burgoyne whotested two complex methods of processing, all bacteria-spotted FTA®Cards brand cellulose based solid matrix in this study were processedwith simple washes.

Bacterial genomic DNA targets amplified directly from washed punchesgave the expected bands (FIG. 1). FTA® Cards brand cellulose based solidmatrix were useful for screening and identifying colonies of Agrobacterbacterium from plants, a gram-negative E. coli bacterium, and adifficult-to-lyse, gram-positive Streptomyces bacterium. Success was duein part to the robust nature of the amplification reaction, notrequiring quantitation of the DNA beforehand. Liquid cultures of thesame bacteria spotted on the cellulose based solid matrix card, such asan FTA® Card, may also work as well as the colonies. Also, transfer ofbacteria by colony lift from the solid growth medium surface with anappropriate-sized cellulose based solid matrix card may be used.Consistent with the known properties of at least one brand cellulosebased solid matrix (i.e., an FTA® Card), bacteria could not be rescuedafter washed, bacteria-spotted punches were placed on solid growth mediaand incubated for >3 days.

Retention of plasmid DNA on FTA® Cards brand cellulose based solidmatrix was tested. Burgoyne reported that purified plasmid DNA spottedon treated paper was efficiently removed with TE buffer (after treatmentwith organic solvents to remove polystyrene protection coating) asmeasured by PCR and transformation (Burgoyne, U.S. Pat. No. 5,496,562).However, using purified DNA did not employ the advantage of directlyspotting plasmid-containing-bacteria on a cellulose based solid matrixcard. Three cultures of E. coli were spotted onto an FTA® Card brandcellulose based solid matrix, and processed punches were amplified.Plasmid DNA as retained on the cellulose based solid matrix card as theexpected amplicons were observed (FIG. 2). However, the amount ofplasmid DNA remaining with the paper is probably low. Standardfluorescent cycle sequencing of plasmid DNA directly from a washed punchdid not detect any signal (data not shown) even though plasmid DNA in asingle colony has been shown to be sufficient for cycle sequencing(Young, A. and Blakesley, R. (1991) Focus 13, 137). However, sequencingof the plasmid DNA could be accomplished after the plasmid DNA wasinitially amplified as described above. Moreover, sequencing may beaccomplished directly from the FTA® brand cellulose based solid matrixsample under appropriate conditions which allow sufficient amounts ofplasmid DNA to be retained on FTA® paper brand cellulose based solidmatrix.

Although some plasmid DNA remained with the FTA® Card brand cellulosebased solid matrix through an extensive wash procedure, it is probablethe DNA is loosely associated and some of it releases during each wash.This was confirmed by generation of the correct amplicon when a 5 μl TEbuffer extraction of a washed punch was amplified by PCR (data notshown). This result suggested that the released plasmid DNA from washedpunches might also be recovered by biological amplification, i.e.,bacterial transformation. DH5α and DH10B cells were each successfullytransformed with 5 μl from a TE buffer extraction of a washed punchpreviously spotted with bacteria harboring one of three plasmids (datanot shown). Successful rescue of the three plasmids to testing a washedpunch introduced directly into the cell transformation reaction (Table3). Transformation reactions tested (two cell types and two DNAintroduction methods) gave comparable results (data not shown). In allcases, bacterial clones were easily recovered, making cellulose basedsolid matrix cards, such as FTA® Cards, potentially very convenient andcost effective for the long term storage of bacterial clones. Similarly,other bacterial clones harboring DNAs such as cosmids, BACs or PACs, canbe recovered from samples archived on these cellulose based solid matrixcards.

TABLE 3 Transformation of DH5α cells with plasmids on an FTA ® cardbrand cellulose based solid matrix punch Plasmid Size (kb) Copy NumberTransformants/punch pSUsrmB2 5.3 6-10  7,000 pJH11104 2.7 ~100 28,000pMAB32 11.2 >100  5,700 Results are the average from 4 dilutions.

Example 2

In an effort to streamline the process required to utilize cellulosebased solid matrix cards for the archiving of vectors, further studieson the transformation of competent cells with plasmid DNA on FTA® Cardsbrand cellulose based solid matrix were undertaken. An overnight cultureof bacterial host cells (DH5α) containing the pSUsrmB2 plasmid werespotted onto FTA® Cards brand cellulose based solid matrix. It wasbelieved that the processing step of the FTA® protocol could beoptimized for samples that do not contain blood (examples of suchsamples are bacterial cells, tissue culture cells, buccal swabs,concentrates of certain body fluids such as saliva or urine, etc). TheFTA® Processing Reagent was initially designed to purify the DNA fromblood samples spotted onto FTA® Cards brand cellulose based solidmatrix. This reagent is required for optimal purification of bloodsamples when enzyme-based assays are utilized to remove heme and otherenzymatic inhibitors.

Modified processing protocols were tested for application in PCR byprocessing punches in a specific manner and then attempting to amplifythe plasmid DNA on the punch using PCR primers (see Table 1) specificfor pSUsrmB2 plasmid DNA. Punches were either not processed in any way,processed according to the manufacturer's directions using three 5minute soaks in FTA® Processing Reagent followed by two 5 minute soaksin TE, or processed using two abbreviated TE rinses. TE was chosen as itis a commonly used biological buffer readily available in thelaboratory, although any solutions or buffer systems (e.g. PBS, TAE,TBE, HEPES, Ringers solution, Dulbecco's Phosphate buffered saline,Earle's balanced salt solution, Gey's balanced salt solution, Hank'sbalanced salt solution, etc., see Life Technologies catalogue) or evenwater may be used in this modified processing method. Preferably,solutions which do not destroy or degrade nucleic acid molecules areused. Amplification was not obtained with punches were unprocessed, butthat punches receiving two brief washes with TE amplified to the samelevel as those processed using the full protocol. It is not unexpectedthat the unprocessed FTA® punch brand cellulose based solid matrix wouldnot produce amplification products since the reagents on the unprocessedpaper would be expected to render the polymerase inactive.

The above results were obtained with standard PCR methodologies that aregenerally not useful for analysis of the relative amounts of DNA in anygiven sample. To determine if there was a difference in the amount ofDNA being retained on the filter with the different processingprocedures, quantitative PCR using the Perkin Elmer 7700 TaqMan machinewas performed. Punch samples (2 mm) were removed from FTA® Cards brandcellulose based solid matrix that contained spots of HeLa cells (5×10⁷cells/ml) dried onto the paper surface. These punches were processedusing either the full protocol or the abbreviated TE washes thensubjected to amplification using the Perkin Elmer b-actin probe andprimers in the TaqMan PCR Reagent Kit (Cat. No. N808-0230, PE AppliedBiosystems, Foster City, Calif.). The signal from the cellulose basedsolid matrix card punches processed using 2 TE washes was consistentlyabout 2-fold higher than the signal from cellulose based solid matrixcard punches that were processed using the manufacturer's directions.

To test streamlining of the processing steps for transformation ofplasmid DNA, 2 mm punches were taken from the FTA® Cards brand cellulosebased solid matrix containing overnight cultures of pSUsrmB2 andprocessed in different manners prior to transformation of competent DH5αcells. Punches were processed either according to the manufacturer'sdirections, or processed using two abbreviated rinses of TE, or usedunprocessed, directly from the cellulose based solid matrix cards. Theresults in Table 4 show that the 2 TE washes produce the maximum numberof colonies per punch but that an unprocessed punch also producessufficient numbers of colonies for archival purposes. The lowest numberof colonies was obtained using the full manufacturer's processingprotocol, again indicating that DNA was being removed from the punchwith the additional washing steps. Additional studies have shown that apunch washed just once in TE gives slightly more colonies than anunprocessed punch and slightly less than a punch washed twice in TE, andadditional TE washes over two decrease the number of colonies obtained.While DNA amplification could not occur with an unprocessed punch,plasmid transformation can, although not as efficiently as with aminimally processed punch. This slight loss of efficiency can beexplained by the loss in viability of some of the competent cells in areaction with an unprocessed punch.

TABLE 4 Punch Processing Protocol Total Colonies per 2 mm Punch*Unprocessed 137 TE washes 193 full processing 45 *average of threeseparate experiments

Example 3

To show the utility of FTA® brand cellulose based solid matrix overother similar collection devices for the archiving of plasmid DNA, anovernight culture of bacterial host cells (DH5α) containing the pSUsrmB2plasmid were spotted onto FTA® cards brand cellulose based solid matrixor similar paperbased collection devices and allowed to air-dry. Theother collection devices used were: Isocode PCR DNA Sample CollectionDevice (Schleicher & Schuell, Keene, N.H.), Generation Capture Card Kit(Gentra Systems, Minneapolis, Minn.) and Whatman #4 filter paper(Clifton, N.J.). Whatman #4 filter paper has been used historically byresearchers for short-term storage of live bacterial cells forapplications such as transfer of a strain of bacteria betweenlaboratories by mail or delivery service. Live bacterial cells can berecovered from the filter paper by placing a portion of the filter paperinto a suitable culture medium for growth.

Punches (2 mm) were taken from each of these collection devices and theFTA® brand cellulose based solid matrix, Isocode and Generation productswere processed according to the manufacturer's directions and with thetwo abbreviated TE washes described above. The Isocode product isdesigned to release DNA from the paper, therefore both the processedpunch as well as a one-tenth volume (5 ml) of the released DNA weretested. The Whatman #4 filter paper punches were not processed in anymanner. The punches were then used in a transformation experiment usingDH5α competent cells. In addition, a TE washed punch (or in the case ofthe Whatman #4 filter paper, an unprocessed punch) was placed into acontrol mock transformation containing 100 ml of SOC medium instead of100 ml of competent cells to test that all the colonies obtained in thetransformation experiments were derived from actual transformationevents and not from carry-over of live bacteria.

The results in Table 5 show that the Gentra Generations product does notproduce numbers of transformants in the same range as FTA® paper brandcellulose based solid matrix. The Isocode product produced numbers ofcolonies in the same range as FTA® paper brand cellulose based solidmatrix, but only when the paper is processed first. The total number ofcolonies obtained will be influenced by copy number and size of theplasmid insert used. As expected, the Whatman #4 paper was an effectivemethod for short-term storage of culturable bacterial cells shown by theequal numbers generated with and without competent cells, but not forlong-term recovery of cells. Due to the nature of FTA® Cards brandcellulose based solid matrix, the DNA stored on FTA® paper brandcellulose based solid matrix is likely to be protected from damage forthe long-term. Bacterial cells on FTA® paper brand cellulose based solidmatrix have shown no loss in transformation efficiency for at least 3months. Blood stored on FTA® paper brand cellulose based solid matrixfor more than 7 years has yielded DNA for PCR analysis.

TABLE 5 Total Number of Colonies per 2 mm Punch (pSUsrmB2 culture)Gentra S&S Whatman Whatman Processing Genera- Iso- #4 #4 Method FTA ®*tion* code (10 days) (25 days) un- 137 2 5 247 0 processed 2 TE 193 5170 N.D. N.D. manu- 45 0 15 N.D. N.D. facturer's protocol released N.D.N.D. 40 N.D. N.D. DNA mock 0 0 0 263 10 transfection *FTA ® and GentraGenerations data is the average of 3 separate experiments N.D.: notdetermined

Example 4

Additional studies on the utility of cellulose based solid matrix paperwith the M13 vector system were undertaken using FTA® paper brandcellulose based solid matrix. M13 is a bacteriophage vector system thathas the ability to produce single stranded DNA molecules that areparticularly useful as DNA sequencing templates. However, preparation ofpurified templates is tedious and time-consuming. These cellulose basedsolid matrix cards were tested to see if they could simplify thepurification of the sequencing template DNA. M13 plaques were eitherdirectly transferred to FTA® paper brand cellulose based solid matrix orhost DH5αF′IQ cells infected with M13 were applied to FTA® paper brandcellulose based solid matrix and allowed to dry. Punches (2 mm) weretaken from these cellulose based solid matrix and processed with TE (asthese samples do not contain blood). After processing, the punches weresubjected to fluorescent automated sequencing using the ABI Prism BigDye Terminator Cycle Sequencing Ready Reaction Kit (Cat. No. 4303149, PEApplied Biosystems, Foster City, Calif.) according to the manufacturer'sdirections and the resulting reactions were analyzed on the ABI Prism377.

An excellent sequence was obtained from the M13 plaque that was directlytransferred to the FTA® Card brand cellulose based solid matrix. Theread-length was greater than 600 nucleotides with no unreadable bases inthe first 600 bases. When this sequence was compared to the knownsequence of M13, there Were 0 errors in the first 300 nucleotides andone error and one misread in the next 300 nucleotides (error rate 0.33%for 600 nucleotides). Sequence data generated from M13 infected cells onFTA® brand cellulose based solid matrix was readable, but lesserror-free indicating that sequence information can be obtained fromthis format, but optimization of cell concentration or processingmethods may be required. M13 plaques placed directly on either GentraGenerations brand cards or Isocode brand cards also produced readablesequences.

The cellulose based solid matrix paper card is known for its utility inarchiving, its ease of sample preparation, and elimination of potentialbiohazards in DNA from blood samples. According to the presentinvention, any matrix or solid medium (preferably a cellulose or paperbased matrix and particularly FTA® Cards brand cellulose based solidmatrix) are also useful for archiving DNA from bacterial sources, bothgenomic and vectors. Thus, the invention represents a method forconvenient and efficient storage, processing and recovery of vector orplasmid clones. This method could be very useful in storage of the vastnumbers of subclones generated, for example, in large-scale genomesequencing projects.

Having now fully described the present invention in some detail by wayof illustration and example for purposes of clarity of understanding, itwill be obvious to one of ordinary skill in the art that the same can beperformed by modifying or changing the invention within a wide andequivalent range of conditions, formulations and other parameterswithout affecting the scope of the invention or any specific embodimentthereof, and that such modifications or changes are intended to beencompassed within the scope of the appended claims.

All publications, patents and patent applications mentioned in thisspecification are indicative of the level of skill of those skilled inthe art to which this invention pertains, and are herein incorporated byreference to the same extent as if each individual publication, patentor patent application was specifically and individually indicated to beincorporated by reference.

1. A method of isolating or purifying one or more plasmids from a hostcell comprising: a) providing a dry matrix or solid medium, wherein saiddry matrix or solid medium further comprises: i) a weak base; ii) achelating agent; and iii) an anionic surfactant or an anionic detergent;b) contacting the matrix or solid medium with a sample comprising a hostcell containing said plasmid or plasmids; c) releasing said one or moreplasmids from said host cell and onto said matrix or solid medium; andd) isolating all or a portion of said plasmid or plasmids from saidmatrix or solid medium.
 2. The method of claim 1, wherein said matrix orsolid medium protects against degradation of said plasmid or plasmids.3. The method of claim 1, wherein said matrix or solid medium comprisesa polymeric matrix or solid medium.
 4. The method of claim 3, whereinthe polymeric matrix or solid medium comprises a cellulose-based matrix.5. The method of claim 3, wherein the polymeric matrix or solid mediumcomprises a micromesh synthetic polymer matrix.
 6. The method of claim5, wherein the polymeric matrix or solid medium comprises a micromeshsynthetic plastic matrix.
 7. The method of claim 1, wherein said matrixor solid matrix is contacted with said one or more cells in solution. 8.The method of claim 1, wherein said matrix or solid medium furthercomprises uric acid or a urate salt.
 9. The method of claim 1, whereinsaid host cells comprise eukaryotic cells.
 10. The method of claim 1,wherein said host cells comprise prokaryotic cells.
 11. The method ofclaim 10, wherein said prokaryotic cells comprise bacterial cells.
 12. Amethod of isolating or purifying one or more plasmids from a host cellcomprising: a) contacting a solid medium with a sample comprising a hostcell containing said plasmid, wherein the solid medium comprises: i) apolymeric matrix comprising a cellulose-based matrix, a micromeshsynthetic polymer matrix, or a micromesh synthetic plastic matrix; ii) aweak base; iii) a chelating agent; and iv) an anionic surfactant or ananionic detergent; b) releasing the plasmid from the host cell and ontosaid medium; and c) isolating said plasmid from said medium.
 13. Themethod of claim 12, wherein said solid medium further comprises uricacid or a urate salt.
 14. A method of isolating or purifying one or moreplasmids from a host cell comprising: a) contacting a solid medium witha sample comprising a host cell containing said plasmid, wherein saidsolid medium protects against degradation of said plasmid and whereinthe solid medium comprises: i) a polymeric matrix comprising acellulose-based matrix, a micromesh synthetic polymer matrix, or amicromesh synthetic plastic matrix; and ii) a composition sorbed to thepolymeric matrix, wherein the composition comprises: a weak base; achelating agent; and an anionic surfactant or an anionic detergent; b)lysing the host cell; c) releasing the plasmid from the host cell andonto said medium; and d) isolating said plasmid from said medium. 15.The method of claim 14, wherein said solid medium further comprises uricacid or a urate salt.
 16. The method of claim 14, wherein said samplecomprises host cells and wherein said host cells comprise eukaryoticcells.
 17. The method of claim 14, wherein said sample comprises hostcells and wherein said host cells comprise prokaryotic cells.
 18. Themethod of claim 12, wherein said sample comprises host cells and whereinsaid host cells comprise eukaryotic cells.
 19. The method of claim 12,wherein said sample comprises host cells and wherein said host cellscomprise prokaryotic cells.